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### Stuff that enables biopieces.

### Initially we need to configure the directories where biopieces are installed
### and where the data (genomes and indexes) that the biopieces work on are installed.
### Allso, it is possible to change the temporary directory from the system's tmp.

export BP_DIR="/Users/m.hansen/biopieces"         # Directory where biopieces are installed
export BP_DATA="/Users/m.hansen/bio_piece_data"   # Contains genomic data etc.
export BP_TMP="/tmp"                              # Required temporary directory.


### The below bin directory should hold biopiece executables - regardsles of programming language.

export BP_BIN="$BP_DIR/bp_bin"              # Directory with biopiece executables.


### The following directories hold the biopiece libraries, modules, gems, etc - one per programming language.

export BP_PERL="$BP_DIR/code_perl"          # Direcotry with Perl code.
export BP_C="$BP_DIR/code_c"                # Direcotry with c code.
export BP_PYTHON="$BP_DIR/code_python"      # Direcotry with Pyton code.
export BP_RUBY="$BP_DIR/code_ruby"          # Direcotry with Ruby code.


### For the Perl modules they may be contributed by different developers, so we define a variable for each.

export BP_PERL_LIBS="$BP_PERL/Maasha"                 # Perl modules from the developer Maasha.
# export BP_PERL_LIBS="$BP_PERL_LIBS:$BP_PERL/<new>"  # Perl modules from a new developer.


### Here we add the biopiece variable to the existing PATH and PERL5LIB variables.

export PATH="$PATH:$BP_BIN"  
export PERL5LIB="$PERL5LIB:$BP_PERL_LIBS"

### Alias allowing power scripting with biopieces.

alias bioscript="perl -MMaasha::Biopieces=read_stream,get_record,put_record -e"


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### Martin A. Hansen, June 2008